Organic acid content is regarded as one of the most important quality traits of fresh tomato (Solanum lycopersicum). However, the complexity of carboxylic acid metabolism and storage means that it is difficult to predict the best way to engineer altered carboxylic acid levels. Here, we used a biochemical analysis of a tomato introgression line with increased levels of fruit citrate and malate at breaker stage to identify a metabolic engineering target that was subsequently tested in transgenic plants. Increased carboxylic acid levels in introgression line 2-5 were not accompanied by changes in the pattern of carbohydrate oxidation by pericarp discs or the catalytic capacity of tricarboxylic acid cycle enzymes measured in isolated mitochondria. However, there was a significant decrease in the maximum catalytic activity of aconitase in total tissue extracts, suggesting that a cytosolic isoform of aconitase was affected. To test the role of cytosolic aconitase in controlling fruit citrate levels, we analyzed fruit of transgenic lines expressing an antisense construct against SlAco3b, one of the two tomato genes encoding aconitase. A green fluorescent protein fusion of SlAco3b was dual targeted to cytosol and mitochondria, while the other aconitase, SlAco3a, was exclusively mitochondrial when transiently expressed in tobacco (Nicotiana tabacum) leaves. Both aconitase transcripts were decreased in fruit from transgenic lines, and aconitase activity was reduced by about 30% in the transgenic lines. Other measured enzymes of carboxylic acid metabolism were not significantly altered. Both citrate and malate levels were increased in ripe fruit of the transgenic plants, and as a consequence, total carboxylic acid content was increased by 50% at maturity.Tomato (Solanum lycopersicum) is an important food crop of high economic value and represents a model species for fleshy fruit physiology and ripening (Giovannoni, 2004;Mueller, 2009). The breeding history of tomato has been dominated by a focus on traits that benefit the grower, such as yield, storage characteristics, and field performance (Schuch, 1994;Giovannoni, 2006; Cong et al., 2008). As a result, there has been an unintentional loss of consumer quality traits such as flavor and nutritional value, and this has focused recent interest on the molecular genetics of such traits (Giovannoni, 2001;Causse et al., 2002 Causse et al., , 2004Fraser et al., 2009;Mounet et al., 2009;Enfissi et al., 2010; Centeno et al., 2011). The accumulation of a range of soluble metabolites is critically important for both flavor and nutrition. Tomato fruit undergo substantial changes in their metabolite content and composition during ripening (Carrari et al., 2006). Fruit flavor is influenced both by volatile and nonvolatile metabolites (Buttery et al., 1987;Goff and Klee, 2006; Carli et al., 2009). Of the nonvolatile metabolites, the balance between sugars and acidic compounds is of major importance for flavor (Tieman et al., 2012). The perceived flavor of tomato fruit is a complex is...